| Updated | Application
| 29 Apr 2024 | VADR updated to version 1.5.1 | VADR stands for Viral Annotation DefineR. It is a suite of tools for classifying and analyzing sequences homologous to a set of reference models of viral genomes or gene families. It has been mainly tested for analysis of Norovirus, Dengue, and SARS-CoV-2 virus sequences in preparation for submission to the GenBank database. 29 Apr 2024 | libvips updated to version 8.15.1 | libvips is a demand-driven, horizontally threaded image processing library. Compared to similar libraries, libvips runs quickly and uses little memory. 26 Apr 2024 | xeniumranger updated to version 2.0.0.12 | Pipeline to process Xenium In Situ Gene Expression data 26 Apr 2024 | rtg-tools updated to version 3.8.4 | variant detection for singletons, families, large pedigrees and populations, cancer, structural variant and CNV analysis, and microbial and metagenomic analysis 26 Apr 2024 | pod5 updated to version 0.3.10 | Tool for manipulating the pod5 format of nanopore reads 23 Apr 2024 | parallel updated to version 20240422 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 22 Apr 2024 | fcs updated to version 0.5.0 | FCS is a toolset to remove contaminant sequences from a genome assembly. 17 Apr 2024 | NAMD updated to version 3.0beta6 | NAMD is a parallel molecular dynamics program for UNIX platforms designed for high-performance simulations in structural biology. VMD, the associated molecular visualization program, is also available. 17 Apr 2024 | GeoMX NGS Pipeline updated to version 3.1.1.6 | The GeoMx NGS Pipeline, processes RNA-sequencing files (FASTQ files) from Illumina sequencers according to parameters defined in the Configuration File (which is generated from the GeoMx DSP run). The Pipeline processes information from these files and outputs .dcc files, which can then be uploaded to the GeoMx DSP system for data analysis. 16 Apr 2024 | manorm updated to version 1.3.0 | MAnorm is for quantitative comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifications. The quantitative binding differences inferred by MAnorm showed strong correlation with both the changes in expression of target genes and the binding of cell type-specific regulators. 14 Apr 2024 | nodejs updated to version 20.12.2 | Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs 14 Apr 2024 | smrtanalysis updated to version 13.1 | SMRT® Analysis is a bioinformatics software suite available for analysis of DNA sequencing data from Pacific Biosciences’ SMRT technology. Users can choose from a variety of analysis protocols that utilize PacBio® and third-party tools. Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences. 12 Apr 2024 | sniffles updated to version 2.3.2 | Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. 9 Apr 2024 | dorado updated to version 0.6.0 | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. 8 Apr 2024 | motioncor3 updated to version 1.0.1 | An improved implementation of MotionCor2 with addition of CTF estimation, Multi-GPU accelerated software package that enables single-pixel level correction of anisotropic beam induced sample motion for cryoEM and cryET images. 6 Apr 2024 | SciTE updated to version 5.4.3 | SciTE or SCIntilla based Text Editor is a cross-platform text editor. Lightweight and built for speed, it is designed mainly for source editing, and performs syntax highlighting and inline function reference for many different languages. 5 Apr 2024 | pangenome updated to version 1.1.2 | nf-core/pangenome is a bioinformatics best-practise analysis pipeline for the rendering of a collection of sequences into a pangenome graph. 5 Apr 2024 | IDL/ENVI updated to version 9.0/6.0 | IDL and ENVI are a complete computing environment for the interactive analysis and visualization of data. IDL integrates an array-oriented language with mathematical analysis and graphical display techniques. ENVI is designed for extracting information from geospatial and medical imagery. 4 Apr 2024 | modkit updated to version 0.2.6 | A bioinformatics tool for working with modified bases from Oxford Nanopore. Specifically for converting modBAM to bedMethyl files using best practices, but also manipulating modBAM files and generating summary statistics. 2 Apr 2024 | tomotwin updated to version 0.8.0 | TomoTwin - a deep metric learning based particle picking procedure for cryo-ET 2 Apr 2024 | hitips updated to version 1.0.4 | HiTIPS: High-Throughput Image Processing Software for the Study of Nuclear Architecture and Gene Expression. Documentations: https://hitips.readthedocs.io/en/latest/ 1 Apr 2024 | csvkit updated to version 1.5.0 | csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats. 1 Apr 2024 | parabricks updated to version 4.3.0 | The Clara Parabricks toolkit is a set of GPU-accelerated genome analysis tools for secondary analysis of next generation sequencing data. 31 Mar 2024 | PartekFlow updated to version 11.0.24.0328 | Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. 29 Mar 2024 | genomad updated to version 1.7.6 | geNomad's primary goal is to identify viruses and plasmids in sequencing data (isolates, metagenomes, and metatranscriptomes). 29 Mar 2024 | minimap2 updated to version 2.28 | Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). 28 Mar 2024 | spaceranger updated to version 3.0.0 | 10x pipeline for processing Visium spatial RNA-seq data 28 Mar 2024 | NeST-VNN updated to version 20240321 | NeST-VNN is an interpretable neural network-based model that predicts cell response to a drug. This framework integrates information across multiple levels of cancer cell biology to understand drug response, and can serve to identify and explain biomarkers for clinical application. 28 Mar 2024 | zstd updated to version 1.5.6 | Zstandard, or zstd as short version, is a fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios. 27 Mar 2024 | stripy-pipeline updated to version 1.2 | STRipy-pipeline is non-graphical command-line version of STRipy that can be integrated into pipelines and analyse multiple STR or VNTR loci in parallel. 27 Mar 2024 | HBD / heme_binder_diffusion updated to version 20240319 | RoseTTAFold All-Atom (RFAA), a deep network capable of modeling full biological assemblies containing proteins, nucleic acids, small molecules, metals, and covalent modifications given the sequences of the polymers and the atomic bonded geometry of the small molecules and covalent modifications. The heme_binder_diffusion pipeline employs RoseTTAFold All-Atom to perform de novo heme binding protein design. 27 Mar 2024 | spipe updated to version 1.20.0 | Split-pool combinatorial barcoding makes it possible to scale projects to hundreds of samples and millions of cells, overcoming limitations of previous droplet based technologies. Spipe (split-pipe) implements combinatorial barcoding method for single cell RNA sequencing (scRNA-seq) with dramatically improved sensitivity. 26 Mar 2024 | cryoDRGN updated to version 1.1.0 | CryoDRGN is an algorithm that leverages the representation power of deep neural networks to directly reconstruct continuous distributions of 3D density maps and map per-particle heterogeneity of single-particle cryo-EM datasets. It contains interactive tools to visualize a dataset’s distribution of per-particle variability, generate density maps for exploratory analysis, extract particle subsets for use with other tools and generate trajectories to visualize molecular motions. 26 Mar 2024 | rapidtide updated to version 2.8.2 | Rapidtide is a suite of Python programs used to model, characterize, visualize, and remove time varying, physiological blood signals from fMRI and fNIRS datasets. The primary workhorses of the package are the rapidtide program, which characterizes bulk blood flow, and happy, which focusses on the cardiac band. 25 Mar 2024 | tedana updated to version 24.0.0 | Tedana is an application to denoise multi-echo fMRI datasets 22 Mar 2024 | DeepLabCut updated to version 2.3.9 | DeepLabCut is an open source toolbox that builds on a state-of-the-art human pose estimation algorithm. It allows training of a deep neural network by using limited training data to precisely track user-defined features, so that the human labeling accuracy will be matched. 22 Mar 2024 | gromacs updated to version 2024.1 | Gromacs is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. 21 Mar 2024 | deepvariant updated to version 1.6.1 | DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. 20 Mar 2024 | bowtie2 updated to version 2.5.3 | A version of bowtie that's particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes 20 Mar 2024 | cutadapt updated to version 4.7 | cutadapt removes adapter sequences from DNA high-throughput sequencing data. This is usually necessary when the read length of the machine is longer than the molecule that is sequenced, such as in microRNA data. 20 Mar 2024 | Tex updated to version 2024 | Tex + Latex + associated packages for high-quality text formatting. 19 Mar 2024 | Beagle updated to version 5.4_01Mar24 | Beagle is a package for imputing genotypes, inferring haplotype phase, and performing genetic association analysis. BEAGLE is designed to analyze large-scale data sets with hundreds of thousands of markers genotyped on thousands of samples. 18 Mar 2024 | model-angelo updated to version 1.0.12 | ModelAngelo is an automatic atomic model building program for cryo-EM maps. 15 Mar 2024 | cellranger updated to version 8.0.0 | Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3’ RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. 14 Mar 2024 | amr updated to version 3.12.8 | AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence. 14 Mar 2024 | mixcr updated to version 4.6.0 | MiXCR is a universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data. 13 Mar 2024 | RoseTTAFold updated to version allatom | Accurate prediction of protein structures and interactions using a 3-track network, , in which information at the 1D sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. 13 Mar 2024 | VEP updated to version 111 | VEP (Variant Effect Predictor) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. 12 Mar 2024 | globus-cli updated to version 3.26.0 | Globus command line interface 12 Mar 2024 | openblas updated to version 0.3.26 | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. 11 Mar 2024 | emready updated to version 2.0 | An application improving the quality and interpretability of cryo-EM maps by local and non-local deep learning. 11 Mar 2024 | snakemake updated to version 8.4.12 | Snakemake aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style. It is well suited for bioinformatic workflows. 10 Mar 2024 | nvchecker updated to version 2.13.1 | nvchecker (short for new version checker) is for checking if a new version of some software has been released. 8 Mar 2024 | scvitools updated to version 1.1.2 | scvi-tools (single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data primarily developed and maintained by the Yosef Lab at UC Berkeley. 5 Mar 2024 | exomiser updated to version 14.0.0 | The Exomiser is a Java program that functionally annotates variants from whole-exome sequencing data starting from a VCF file. 5 Mar 2024 | difftf updated to version 1.9 | Genome-wide quantification of differential transcription factor activity 4 Mar 2024 | FEBio updated to version 4.4 | FEBio software suite implement a nonlinear implicit finite element (FE) framework, designed specifically for analysis in computational solid biomechanics. FEBio offers modeling scenarios, constitutive models, and boundary conditions, which are relevant to numerous applications in biomechanics. The open-source FEBio software is written in C++, with particular attention to scalar and parallel performance on modern computer architectures. 4 Mar 2024 | Rosetta updated to version 2023.45 | The Rosetta++ software suite can perform de novo protein structure predictions, identify low free energy sequences for target protein backbones, predict the structure of a protein-protein complex from the individual structures of the monomer components, incorporate NMR data into the basic Rosetta protocol to accelerate the process of NMR structure prediction, and more... 4 Mar 2024 | pyem updated to version 240209 | UCSF pyem is a collection of Python modules and command-line utilities for electron microscopy of biological samples. 4 Mar 2024 | mc updated to version 4.8.31 | GNU Midnight Commander is a visual file manager, with a feature rich full-screen text mode application that allows you to copy, move and delete files and whole directory trees, search for files and run commands in the subshell. Type module load mc and then the command mc to get started. 4 Mar 2024 | autoconf updated to version 2.72 | Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. 4 Mar 2024 | gnuplot updated to version 6.0.0 | Gnuplot is a portable command-line driven graphing utility to visualize mathematical functions and data interactively, and can support many non-interactive uses such as web scripting. Type 'gnuplot' to run, or 'module avail gnuplot' to see other available versions. 3 Mar 2024 | RepeatMasker updated to version 4.1.6 | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. 1 Mar 2024 | tortoisev4 updated to version current | TORTOISE (Tolerably Obsessive registration and Tensor Optimization Indolent Software Ensemble) is a suite of programs for for pre-processing, post-processing and analyzing diffusion MRI data 29 Feb 2024 | mpich updated to version 4.1.3 | MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (both MPI-1 and MPI-2). 29 Feb 2024 | boost updated to version 1.84 | Boost provides free peer-reviewed portable C++ source libraries. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. 29 Feb 2024 | Julia updated to version 1.10.1 | high level, dynamic language for technical computing 28 Feb 2024 | quarto updated to version 1.4.550 | Quarto is an open-source scientific and technical publishing system built on Pandoc 28 Feb 2024 | lazygit updated to version 0.40.2 | A simple terminal UI for git commands 28 Feb 2024 | SignatureAnalyzer updated to version 20240208 | SignatureAnalyzer is a tool for the identification of somatic mutational signatures. It employs Bayesian non-negative matrix factorization (NMF). 26 Feb 2024 | slapnap updated to version 20210507 | The slapnap container is a tool for using the Compile, Analyze and Tally NAb Panels (CATNAP; Yoon et al. 2015) database to develop predictive models of HIV-1 neutralization sensitivity to one or several broadly neutralizing antibodies (bnAbs). 26 Feb 2024 | pySCENIC updated to version 0.12.1 | pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering). It enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data. 26 Feb 2024 | glog updated to version 0.7.0 | The glog library implements application-level logging. This library provides logging APIs based on C++-style streams and various helper macros. 26 Feb 2024 | JAX-CNV updated to version 20240208 | JAX-CNV implemens an algorithm for copy number variant (CNV) calling from the whole-genome sequencing (WGS) data. On testing data, it demonstrated ~7-fold increase in the number of detected CNVs as compared to the chromosomal microarray assay (CMA) for clinical diagnosis. 21 Feb 2024 | NucleoATAC updated to version 0.3.4 | NucleoATAC is a software for nucleosome calling using ATAC-seq. It can identify the rotational and translational positions of nucleosomes with up to base-pair resolution and provide quantitative measures of nucleosome occupancy. 20 Feb 2024 | famsa updated to version 2.2.2 | Progressive algorithm for large-scale multiple sequence alignments 16 Feb 2024 | rust updated to version 1.76.0 | A language empowering everyone to build reliable and efficient software. 15 Feb 2024 | fastqc updated to version 0.12.1 | It provide quality control functions to next gen sequencing data. 15 Feb 2024 | bamreadcount updated to version 1.0.1 | Bam-readcount generates metrics at single nucleotide positions. There are number of metrics generated which can be useful for filtering out false positive calls. 15 Feb 2024 | synapseclient updated to version 4.0.0 | The synapseclient package provides an interface to Synapse, a collaborative workspace for reproducible, data intensive research projects 15 Feb 2024 | percolator updated to version rel-3-06-05 | A software for postprocessing of shotgun proteomics data 14 Feb 2024 | nda-tools updated to version 0.2.12,0.2.16,0.2.26 | In order to submit data to the National Institute of Mental Health Data Archives (NDA), users must validate their data to ensure it complies with the required format. This is done using the NDA validation tool, vtcmd. Additionally, users can package and download data from NDA as well, using the downloadcmd tool. 13 Feb 2024 | sambamba updated to version 1.0.1 | Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current parallelised functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth. |